NOTE : Per default the clustering is made on the BACKBONE of a PROTEIN
PLEASE READ THE DOCUMENTATION AT https://www.github.com/tubiana/TTClust FOR PROPER USAGE
======= TRAJECTORY READING =======
====== Clustering ========
creating distance matrix
NOTE : Extraction of subtrajectory for time optimisation
..............................................................................................................................................................................................................
Calculation ended - saving distance matrix
Saving distance matrix : backbone.npy
Matrix shape: (50000, 50000)
Scipy linkage in progress. Please wait. It can be long
The distance has been tested and is VALID. Ignore the next ClusterWarning message from scipy.
Killed
What I can do?
Thanks.
Saverio
P.S.
$ ls -lh
total 9,4G
-rw-rw-r-- 1 xxxx xxxx 9,4G ago 27 21:24 backbone.npy
drwxrwxr-x 2 xxxx xxxx 4,0K ago 27 18:46 clustering
Hi, I have a problem with the following command:
$ python /home/xxxx/miniconda3/bin/ttclust -f ../10_prod_md_step_000-1000_ns_strip_wat_autoimage_amber_tut.nc -t ../target_strip_wat_autoimage_amber_tut_000_1000_ns.prmtop
** TTCLUST 4.10.3 *****
NOTE : Per default the clustering is made on the BACKBONE of a PROTEIN PLEASE READ THE DOCUMENTATION AT https://www.github.com/tubiana/TTClust FOR PROPER USAGE
======= TRAJECTORY READING ======= ====== Clustering ======== creating distance matrix NOTE : Extraction of subtrajectory for time optimisation .............................................................................................................................................................................................................. Calculation ended - saving distance matrix Saving distance matrix : backbone.npy Matrix shape: (50000, 50000) Scipy linkage in progress. Please wait. It can be long The distance has been tested and is VALID. Ignore the next ClusterWarning message from scipy. Killed
What I can do? Thanks.
Saverio
P.S. $ ls -lh total 9,4G -rw-rw-r-- 1 xxxx xxxx 9,4G ago 27 21:24 backbone.npy drwxrwxr-x 2 xxxx xxxx 4,0K ago 27 18:46 clustering
$ cat /proc/meminfo MemTotal: 65694696 kB MemFree: 61807048 kB MemAvailable: 62023376 kB Buffers: 30172 kB Cached: 688492 kB SwapCached: 230896 kB Active: 1915300 kB Inactive: 699536 kB Active(anon): 1236680 kB Inactive(anon): 692276 kB Active(file): 678620 kB Inactive(file): 7260 kB Unevictable: 3104 kB Mlocked: 16 kB SwapTotal: 12582908 kB SwapFree: 10972056 kB Zswap: 0 kB Zswapped: 0 kB Dirty: 8 kB Writeback: 0 kB AnonPages: 1848536 kB Mapped: 455740 kB Shmem: 32784 kB KReclaimable: 261980 kB Slab: 635524 kB SReclaimable: 261980 kB SUnreclaim: 373544 kB KernelStack: 33264 kB PageTables: 89204 kB SecPageTables: 0 kB NFS_Unstable: 0 kB Bounce: 0 kB WritebackTmp: 0 kB CommitLimit: 45430256 kB Committed_AS: 27634884 kB VmallocTotal: 34359738367 kB VmallocUsed: 131588 kB VmallocChunk: 0 kB Percpu: 124416 kB HardwareCorrupted: 0 kB AnonHugePages: 0 kB ShmemHugePages: 0 kB ShmemPmdMapped: 0 kB FileHugePages: 0 kB FilePmdMapped: 0 kB Unaccepted: 0 kB HugePages_Total: 0 HugePages_Free: 0 HugePages_Rsvd: 0 HugePages_Surp: 0 Hugepagesize: 2048 kB Hugetlb: 0 kB DirectMap4k: 1381140 kB DirectMap2M: 28921856 kB DirectMap1G: 36700160 kB